Signatures of selective sweeps in urban and rural white clover populations

Urbanization is increasingly recognized as a powerful force of evolutionary change. However, anthropogenic sources of selection can often be similarly strong and multifarious in rural habitats, but these are often ignored in studies of urban evolutionary ecology. Despite numerous examples of phenotypic differentiation between urban and rural populations, we still lack an understanding of the genes enabling adaptation to these contrasting habitats and the genetic architecture underlying urban and rural adaptation. In this study, we conducted whole genome sequencing of 120 urban, suburban, and rural white clover plants from Toronto, Canada. We used these data to identify signatures of selective sweeps across the genome using both SFS and haplotype-based approaches, and characterize the architecture of selective sweeps. We found evidence for selection in genomic regions involved in abiotic stress tolerance and growth/development in both urban and rural populations. Urban and rural populations did not differ in the proportion of hard vs. soft sweeps, though urban populations were characterized by wider sweeps, which may indicate differences in the strength or timescale of selection. In addition, patterns of allele frequency and haplotype differentiation suggest that most sweeps are incomplete. These results highlight how both urban and rural habitats are driving ongoing selection in white clover populations, and motivate future work disentangling the genetic architecture of ecologically important phenotypes, and estimating the strength and timescale of selection underlying adaptation to contemporary anthropogenic habitats.